Update Manuscripts/2021b docs

docs/pages/manuscripts/2021b/2021b.md

@@ -1,11 +1,20 @@
 ---
 title: 2021b
-has_children: False
+has_children: True
 nav_order: 2
 parent: Manuscripts
 ---
 
 # 2021b
 {:.no_toc}
 
+* TOC
+{:toc}
+
+This page shows how to reproduce: 
+
++ Tension-pCa curves with and without an MyBPC SRX stabilizing effect/actin binding effect
++ A Mavacamten dose-dependent response curve
++ Slack-restretch (k_tr) simulations for 1 or 3 potential binding sites for myosin
+
 

docs/pages/manuscripts/2021b/Mavacamten/Mavacamten.md

@@ -0,0 +1,50 @@
+---
+title: Mavacamten
+has_children: False
+nav_order: 2
+parent: 2021b
+grand_parent: Manuscripts
+---
+
+# Mavacamten
+
+This page shows how to reproduce a dose-dependent response curve to a myotrope (Mavacamten).
+
+## Getting ready
+
++ Open an Anaconda Prompt
+
++ Activate the FiberSim Anaconda Environment by executing:
+```
+conda activate fibersim
+```
++ Change directory to `<FiberSim_dir>/code/FiberPy/FiberPy`, where `<FiberSim_dir>` is the directory where you installed FiberSim.
+
+## Run the simulations
+
++ Type:
+ ```
+python FiberPy.py run_batch "../../../manuscripts/2021b/myotrope/batch_mava.json"
+ ```
+
++ You should see text appearing in the terminal window, showing that the simulations are running. When it finishes (this may take ~15 min), you should see something similar to the image below.
+
+![command prompt](command_prompt.PNG)
+
+## Viewing the results
+
+The dose-dependent response is stored in `<FiberSim_dir>/manuscripts/2021b/myotrope/sim_output` 
+
+<img src='mava_dose_response.png' width="50%">
+
+The underlying data are stored in `<FiberSim_dir>/manuscripts/2021b/myotrope/sim_output/analysis.xlsx`
+
+<img src='analysis.PNG' width="40%">
+
+The 10 subfolders from `<FiberSim_dir>/manuscripts/2021b/myotrope/sim_output` contain the simulations results and summary figures for each Mavacamten concentration.
+
+![sim_output](sim_output.PNG)
+
+
+
+

docs/pages/manuscripts/2021b/MyBPC/MyBPC.md

@@ -0,0 +1,60 @@
+---
+title: MyBPC
+has_children: False
+nav_order: 1
+parent: 2021b
+grand_parent: Manuscripts
+---
+
+# MyBPC
+
+This page shows how to reproduce 4 tension-pCa curves corresponding to 4 conditions:
+
++ Base case 
++ MyBPC stabilizing SRX
++ MyBPC binding to actin
++ MyBPC stabilizing SRX + binding to actin
+
+
+## Getting ready
+
++ Open an Anaconda Prompt
+
++ Activate the FiberSim Anaconda Environment by executing:
+```
+conda activate fibersim
+```
++ Change directory to `<FiberSim_dir>/code/FiberPy/FiberPy`, where `<FiberSim_dir>` is the directory where you installed FiberSim.
+
+## Run the simulations
+
++ Type:
+ ```
+python FiberPy.py run_batch "../../../manuscripts/2021b/MyBPC/batch_pCa_curves.json"
+ ```
+
++ You should see text appearing in the terminal window, showing that the simulations are running. When it finishes (this may take ~1-2 hour), you should see something similar to the image below.
+
+![command prompt](command_prompt.PNG)
+
+## Viewing the results
+
+The tension-pCa curves for the four cases are saved in `<FiberSim_dir>/manuscripts/2021b/MyBPC/sim_output/force_pCa_curves.png`.
+
+The normalized tension-pCa curves are saved in `<FiberSim_dir>/manuscripts/2021b/MyBPC/sim_output/force_pCa_curves_normalized.png`.
+
+<img src='force_pCa_curves.png' width="40%">
+<img src='force_pCa_curves_normalized.png' width="55%">
+
+The underlying data are stored in `<FiberSim_dir>/manuscripts/2021b/MyBPC/sim_output/analysis.xlsx`.
+
+<img src='analysis.PNG' width="30%">
+
+The 4 subfolders from `<FiberSim_dir>/manuscripts/2021b/MyBPC/sim_output` contain the simulations results and summary figures for each pCa value in each case (base, MyBPC stabilized SRX, MyBPC actin binding, and MyBPC stabilized SRX + MyBPC actin binding).
+
+![subfolder](subfolder.PNG)
+
+
+
+
+

docs/pages/manuscripts/2021b/k_tr/k_tr.md

@@ -0,0 +1,55 @@
+---
+title: k_tr
+has_children: False
+nav_order: 3
+parent: 2021b
+grand_parent: Manuscripts
+---
+
+# k_tr
+
+This page shows how to reproduce a slack/re-stretch simulation for two conditions:
+
++ Myosin heads are able to bind to the nearest actin binding site only (1 potential binding site)
+
++ Myosin heads are able to bind to one of the three nearest acting binding sites (3 potential binding sites)
+
+## Getting ready
+
++ Open an Anaconda Prompt
+
++ Activate the FiberSim Anaconda Environment by executing:
+```
+conda activate fibersim
+```
++ Change directory to `<FiberSim_dir>/code/FiberPy/FiberPy`, where `<FiberSim_dir>` is the directory where you installed FiberSim.
+
+## Run the simulations
+
++ Type:
+ ```
+python FiberPy.py run_batch "../../../manuscripts/2021b/k_tr/batch_k_tr.json"
+ ```
+
++ You should see text appearing in the terminal window, showing that the simulations are running. When it finishes (this may take ~20 min), you should see something similar to the image below.
+
+![command prompt](command_prompt.PNG)
+
+## Viewing the results
+
+The figure showing results for both simulations is stored in `<FiberSim_dir>/manuscripts/2021b/k_tr/sim_output/superposed_summary.png`
+
+<img src='superposed_summary.png' width="50%">
+
+Summary figures and results files for the individual simulations are also stored in `<FiberSim_dir>/manuscripts/2021b/k_tr/sim_output`.
+
+![sim_output](sim_output.PNG)
+
+<figure class="left">
+  <img src="summary_1.png" width="45%"/>
+  <img src="summary_2.png" width="45%"/>
+</figure>
+
+
+
+

manuscripts/2021b/MyBPC/sim_input/3/pCa_48/output_handler_48.json

@@ -3,7 +3,7 @@
         {
             "relative_to": "this_file",
             "template_file_string": "../../../template/template_summary.json",
-            "output_file_string": "../../../sim_output\\1\\summary_48.png"
+            "output_file_string": "../../../sim_output\\3\\summary_48.png"
         }
     ]
 }

manuscripts/2021b/MyBPC/sim_input/3/pCa_52/output_handler_52.json

@@ -3,7 +3,7 @@
         {
             "relative_to": "this_file",
             "template_file_string": "../../../template/template_summary.json",
-            "output_file_string": "../../../sim_output\\1\\summary_52.png"
+            "output_file_string": "../../../sim_output\\3\\summary_52.png"
         }
     ]
 }

manuscripts/2021b/MyBPC/sim_input/3/pCa_56/output_handler_56.json

@@ -3,7 +3,7 @@
         {
             "relative_to": "this_file",
             "template_file_string": "../../../template/template_summary.json",
-            "output_file_string": "../../../sim_output\\1\\summary_56.png"
+            "output_file_string": "../../../sim_output\\3\\summary_56.png"
         }
     ]
 }

manuscripts/2021b/MyBPC/sim_input/3/pCa_58/output_handler_58.json

@@ -3,7 +3,7 @@
         {
             "relative_to": "this_file",
             "template_file_string": "../../../template/template_summary.json",
-            "output_file_string": "../../../sim_output\\1\\summary_58.png"
+            "output_file_string": "../../../sim_output\\3\\summary_58.png"
         }
     ]
 }

manuscripts/2021b/MyBPC/sim_input/3/pCa_62/output_handler_62.json

@@ -3,7 +3,7 @@
         {
             "relative_to": "this_file",
             "template_file_string": "../../../template/template_summary.json",
-            "output_file_string": "../../../sim_output\\1\\summary_62.png"
+            "output_file_string": "../../../sim_output\\3\\summary_62.png"
         }
     ]
 }

manuscripts/2021b/MyBPC/sim_input/3/pCa_70/output_handler_70.json

@@ -3,7 +3,7 @@
         {
             "relative_to": "this_file",
             "template_file_string": "../../../template/template_summary.json",
-            "output_file_string": "../../../sim_output\\1\\summary_70.png"
+            "output_file_string": "../../../sim_output\\3\\summary_70.png"
         }
     ]
 }

manuscripts/2021b/MyBPC/sim_input/4/pCa_48/output_handler_48.json

@@ -3,7 +3,7 @@
         {
             "relative_to": "this_file",
             "template_file_string": "../../../template/template_summary.json",
-            "output_file_string": "../../../sim_output\\1\\summary_48.png"
+            "output_file_string": "../../../sim_output\\4\\summary_48.png"
         }
     ]
 }

manuscripts/2021b/MyBPC/sim_input/4/pCa_52/output_handler_52.json

@@ -3,7 +3,7 @@
         {
             "relative_to": "this_file",
             "template_file_string": "../../../template/template_summary.json",
-            "output_file_string": "../../../sim_output\\1\\summary_52.png"
+            "output_file_string": "../../../sim_output\\4\\summary_52.png"
         }
     ]
 }

manuscripts/2021b/MyBPC/sim_input/4/pCa_56/output_handler_56.json

@@ -3,7 +3,7 @@
         {
             "relative_to": "this_file",
             "template_file_string": "../../../template/template_summary.json",
-            "output_file_string": "../../../sim_output\\1\\summary_56.png"
+            "output_file_string": "../../../sim_output\\4\\summary_56.png"
         }
     ]
 }

manuscripts/2021b/MyBPC/sim_input/4/pCa_58/output_handler_58.json

@@ -3,7 +3,7 @@
         {
             "relative_to": "this_file",
             "template_file_string": "../../../template/template_summary.json",
-            "output_file_string": "../../../sim_output\\1\\summary_58.png"
+            "output_file_string": "../../../sim_output\\4\\summary_58.png"
         }
     ]
 }

manuscripts/2021b/MyBPC/sim_input/4/pCa_62/output_handler_62.json

@@ -3,7 +3,7 @@
         {
             "relative_to": "this_file",
             "template_file_string": "../../../template/template_summary.json",
-            "output_file_string": "../../../sim_output\\1\\summary_62.png"
+            "output_file_string": "../../../sim_output\\4\\summary_62.png"
         }
     ]
 }

manuscripts/2021b/MyBPC/sim_input/4/pCa_70/output_handler_70.json

@@ -3,7 +3,7 @@
         {
             "relative_to": "this_file",
             "template_file_string": "../../../template/template_summary.json",
-            "output_file_string": "../../../sim_output\\1\\summary_70.png"
+            "output_file_string": "../../../sim_output\\4\\summary_70.png"
         }
     ]
 }

manuscripts/2021b/MyBPC/template/template_summary.json

@@ -30,7 +30,7 @@
             {
                 "label": "pCa",
               "scaling_type": "close_fit",
-              "ticks": [ 9, 5.6 ],
+              "ticks": [ 9, 4 ],
                 "series":
                 [
                     {
@@ -43,7 +43,6 @@
             "column": 1,
           "y_info": {
             "label": "Force \n (kN m$^{\\mathregular{-2}}$)",
-            "ticks": [ 0, 90 ],
             "series": [
               {
                 "field": "force",

manuscripts/2021b/k_tr/batch_k_tr.json

@@ -30,7 +30,8 @@
           "results_folder": "sim_output",
           "output_image_file_string": "sim_output/superposed_summary.png",
           "formatting": {
-            "color_set": [ "#0033a0", "#a0001b" ]
+            "color_set": [ "#0033a0", "#a0001b" ],
+            "labels":  ["1 BS", "2 BS"]
           }
 
         }

manuscripts/2021b/k_tr/template/template_summary.json

@@ -39,7 +39,7 @@
       "column": 1,
       "y_info": {
         "label": "HS length\n(nm)",
-        "ticks": [ 1080, 1110 ],
+        "ticks": [ 980, 1010 ],
         "series": [
           {
             "field": "hs_length"